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At least 253 records · Page 14

Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies

Vaccination strategies aimed at maturing broadly neutralizing antibodies (bnAbs) from naïve precursors are hindered by unusual features that characterize these Abs, including insertions and deletions (indels). Longitudinal studies of natural HIV infection cases shed light on the complex processes underlying bnAb development and have suggested a role for superinfection as a potential enhancer of neutralization breadth. Here we describe the development of a potent bnAb lineage that was elicited by two founder viruses to inform vaccine design. The V3-glycan targeting bnAb lineage (PC39-1) was isolated from subtype C-infected IAVI Protocol C elite neutralizer, donor PC39, and is defined by the presence of multiple independent insertions in CDRH1 that range from 1-11 amino acids in length. Memory B cell members of this lineage are predominantly atypical in phenotype yet also span the class-switched and antibody-secreting cell compartments. Development of neutralization breadth occurred concomitantly with extensive recombination between founder viruses before each virus separated into two distinct population “arms” that evolved independently to escape the PC39-1 lineage. Ab crystal structures show an extended CDRH1 that can help stabilize the CDRH3. Overall, these findings suggest that early exposure of the humoral system to multiple related Env molecules could promote the induction of bnAbs by focusing Ab responses to conserved epitopes.

59 BASIC BIOLOGICAL SCIENCES↗

Evolution of Charge-Lattice Dynamics across the Kuramoto Synchronization Phase Diagram of Quantum Tunneling Polarons in Cuprate Superconductors

Because of its sensitivity to the instantaneous structure factor, S(Q,t = 0), Extended X-ray Absorption Fine Structure (EXAFS) is a powerful tool for probing the dynamic structure of condensed matter systems in which the charge and lattice dynamics are coupled. When applied to hole-doped cuprate superconductors, EXAFS has revealed the presence of internal quantum tunneling polarons (IQTPs). An IQTP arises in EXAFS as a two-site distribution for certain Cu–O pairs, which is also duplicated in inelastic scattering but not observed in standard diffraction measurements. The Cu–Sr pair distribution has been found to be highly anharmonic and strongly correlated to both the IQTPs and to superconductivity, as, for example, in YSr 2 Cu 2.75 Mo 0.25 O 7.54 (T c =84 K). In order to describe such nontrivial, anharmonic charge-lattice dynamics, we have proposed a model Hamiltonian for a prototype six-atom cluster, in which two Cu-apical-O IQTPs are charge-transfer bridged through Cu atoms by an O atom in the CuO 2 plane and are anharmonically coupled via a Sr atom. By applying an exact diagonalization procedure to this cluster, we have verified that our model indeed produces an intricate interplay between charge and lattice dynamics. Then, by using the Kuramoto model for the synchronization of coupled quantum oscillators, we have found a first-order phase transition for the IQTPs into a synchronized, phase-locked phase. Most importantly, we have shown that this transition results specifically from the anharmonicity. Finally, we have provided a phase diagram showing the onset of the phase-locking of IQTPs as a function of the charge-lattice and anharmonic couplings in our model. We have found that the charge, initially confined to the apical oxygens, is partially pumped into the CuO 2 plane in the synchronized phase, which suggests a possible connection between the synchronized dynamic structure and high-temperature superconductivity (HTSC) in doped cuprates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The TW Hya Rosetta Stone Project. I. Radial and Vertical Distributions of DCN and DCO{sup +}

Molecular D/H ratios are frequently used to probe the chemical past of solar system volatiles. Yet it is unclear which parts of the solar nebula hosted an active deuterium fractionation chemistry. To address this question, we present 0."2–0."4 Atacama Large Millimeter/submillimeter Array (ALMA) observations of DCO{sup +} and DCN 2–1, 3–2, and 4–3 toward the nearby protoplanetary disk around TW Hya, taken as part of the TW Hya Rosetta Stone project, augmented with archival data. DCO{sup +} is characterized by an excitation temperature of ~40 K across the 70 au radius pebble disk, indicative of emission from a warm, elevated molecular layer. Tentatively, DCN is present at even higher temperatures. Both DCO{sup +} and DCN present substantial emission cavities in the inner disk, while in the outer disk the DCO{sup +} and DCN morphologies diverge: most DCN emission originates from a narrow ring peaking around 30 au, with some additional diffuse DCN emission present at larger radii, while DCO{sup +} is present in a broad structured ring that extends past the pebble disk. Based on a set of simple parametric disk abundance models, these emission patterns can be explained by a near-constant DCN abundance exterior to the cavity, and an increasing DCO{sup +} abundance with radius. In conclusion, the ALMA observations reveal an active deuterium fractionation chemistry in multiple disk regions around TW Hya, but not in the cold planetesimal-forming midplane and in the inner disk. More observations are needed to explore whether deuterium fractionation is actually absent in these latter regions, and if its absence is a common feature or something peculiar to the old TW Hya disk.

36 MATERIALS SCIENCE↗

2.1.2.403 - Fatigue and Structural Load Analysis and Control for Variable-Geometry Wave Energy Converters (VGWECs)

The VGWEC project will generate and disseminate the foundational knowledge enabling a paradigm shift in the design of wave energy converters (WECs) by adding a geometry control option on top of power-take-off load control. The variable-geometry modules (VGMs) provide control over a WEC's hydrodynamics that can emphasize power absorption or load shedding. Additional load shedding provided by the VGMs is expected to reduce the device structural mass and extend the sea state operating envelope, by limiting peak loading, both contributing towards reducing levelized cost of energy (LCOE) estimates.

hydrodynamic↗

Pre-Equilibrium De-Excitations for Neutrino-Nucleus Interactions

The Deep Underground Neutrino Experiment (DUNE) is sensitive to MeV-scale energy depositions from low-energy astrophysical neutrinos, including those from core-collapse supernovae. Interpreting these detector signals requires accurate modeling of the nuclear de-excitation that follows from the neutrino-nucleus interaction. The MARLEY (Model of Argon Reaction Low-Energy Yields) event generator specializes in the low-energy regime. MARLEY currently assumes the residual nucleus equilibrates immediately after the primary interaction. This omits the intermediate pre-equilibrium stage in which energy redistributes among nucleons until statistical equilibrium is reached. While pre-equilibrium effects are well established for nucleon-induced reactions, they have not previously been studied for neutrino-nucleus interactions. This work addresses that gap by implementing a two-component exciton model, which is the first dedicated treatment of pre-equilibrium de-excitation for neutrino-nucleus interactions, restructured around MARLEY's existing class hierarchy to prepare for direct integration, including particle-hole state densities, internal transition rates, and pre-equilibrium particle emission. The calculations show encouraging agreement with the TALYS-2.2 nuclear reaction code for neutron-nucleus interactions. We further propose a concrete integration path into the full MARLEY event generator, including derived class structure and an extended event record for pre-equilibrium vertices in support of future reweighting. Remaining work focuses on refining the emission width calculation, adding $\gamma$-ray emission, and completing this integration to quantify the impact of pre-equilibrium effects on the expected low-energy neutrino signals in DUNE and similar experiments.

Visser, Erin [Michigan State U., East Lansing (mai↗

Selenium Migration and Local Structures in Cu‐Doped CdSeTe Solar Cells after Aging

Selenium grading plays a critical role in state-of-the-art Cadmium Telluride photovoltaic cells by enhancing long-wavelength absorption and extending minority carrier lifetimes —key to enabling the current performance record of 23.08%. However, very little is understood about selenium motion. In this study, a comprehensive, multimodal, and multiscale approach is employed to investigate Se migration and local structural changes in copper (Cu)-doped CdSeTe solar cells subjected to accelerated stress. X-ray fluorescence (XRF) microscopy shows unexpected levels of Se diffusion after 500 h under heat (75°C) and light (0.8 suns, 80 mW/cm 2 ), suggesting the coexistence of fast and slow diffusion channels even at low temperatures, with unexpectedly low activation energies (<0.85 eV). X-ray Absorption Near Edge Structure (XANES) analysis indicates a preferential migration of Se atoms to anionic lattice sites and a reduction in Se-Cl co-passivation at Te-terminated dislocation cores. Furthermore, these findings point to a reconfiguration of Se local environments and highlight the potential role of extended structural defects in enabling Se transport at low temperatures. Additionally, XANES results suggest that the presence of metallic Cu across the absorber layer may contribute to back-contact degradation and reduced hole density in both fresh and aged devices.

14 SOLAR ENERGY↗

The status of the Japanese material properties handbook and the challenge to facilitate structural design criteria for DEMO in-vessel components

This work summarizes the current status of the material properties handbook for a structural design using Japanese reduced-activation ferritic/martensitic steel F82H. Specifically, the key structural parameters, e.g. time-independent/dependent design stresses and fatigue design curves, were determined by following the French structural design code RCC-MRx. Moreover, under the Japan–U.S. collaboration, tensile data were newly added to the benchmark heavy irradiation data up to 80 dpa, as critical input information in the intermediate check and review in Japan. Furthermore, the status of structural material data and the near-term and long-term issues were clarified by the evaluation using the attribute guides. In parallel, the structural design approaches, which were newly introduced and extended to cope with the structural design issues under the complex environmental conditions peculiar to the DEMO reactor, were noted with the initial R&D results. Of the many design issues, the multi-axial loading conditions due to the complexity of the DEMO reactor as well as the coolant compatibility and the irradiation effect are mentioned. For example, in the paper, multi-axial fatigue–creep testing and evaluation using the modified universal slope method and brittle/ductile fracture testing and evaluation using the local approach are explained toward DEMO.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Elucidating the Structure of the Eu‐EDTA Complex in Solution at Various Protonation States

Abstract Ethylenediaminetetraacetic acid (EDTA), which has two amine and four carboxylate protonation sites, forms stable complexes with lanthanide ions. This work analyzes the coordination structure, in atomic resolution, of the Eu 3+ ion complexed with EDTA in all its protonation states in aqueous solution. Eu‐EDTA complexes were modeled using classical molecular dynamics (MD) simulations using force field parameters optimized with ab initio molecular dynamics (AIMD) simulations. Structures from the MD simulations were used to predict extended X‐ray absorption fine structure (EXAFS) spectra and compared with EXAFS measurements of the Eu 3+ aqua ion and Eu‐EDTA complexes at pH 3 and 11. This work details how Eu‐EDTA complex coordination structures change with increasing protonation of the EDTA ligand in the complex, from the tightly bound unprotonated complex to the unbinding of the fully protonated EDTA ligand from the Eu 3+ ion as both become solvated by water. Agreement between predicted and measured EXAFS spectra supports the findings from simulation.

Chemistry↗

Blueprinting extendable nanomaterials with standardized protein blocks

A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies, in comparison, has been much more complex, largely owing to the irregular shapes of protein structures. Here we describe extendable linear, curved and angled protein building blocks, as well as inter-block interactions, that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight ‘train track’ assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence–structure relationships, it has not previously been possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank three-dimensional canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to ‘back of an envelope’ architectural blueprints.

36 MATERIALS SCIENCE↗

Unified descriptor for enhanced critical heat flux during pool boiling of hemi-wicking surfaces

Boiling heat transfer is dictated by interfacial phenomena at the three-phase contact line where vapor bubbles form on the surface. Structured surfaces have shown significant enhancement in critical heat flux (CHF) during pool boiling by tailoring interfacial phenomena. This CHF enhancement has been primarily explained by two structural effects: roughness, which extends the contact line length at the bubble base, and wickability, the ability to imbibe liquid through surface structures by capillary pumping. Here, in this work, we show that CHF enhancement on structured surfaces cannot be described by roughness or wickability alone. This result was confirmed using systematically designed micropillar surfaces with controlled roughness and wickability. Further, we performed a scaling analysis and derived a unified descriptor, which represents the combined effects of thin film density and volumetric wicking rate. This unified descriptor shows a reasonable correlation with CHF values with our experiments and literature data. This work provides important insights in understanding the role of surface structures on CHF enhancement, thereby providing guidelines for the systematic design of surface structures for enhanced pool boiling heat transfer.

42 ENGINEERING↗

X-ray Spectroscopy Fingerprints of Pristine and Functionalized Graphene

In this work, we demonstrate how to identify and characterize the atomic structure of pristine and functionalized graphene materials from a combination of computational simulation of X-ray spectra, on the one hand, and computer-aided interpretation of experimental spectra, on the other. Despite the enormous scientific and industrial interest, the precise structure of these 2D materials remains under debate. As we show in this study, a wide range of model structures from pristine to heavily oxidized graphene can be studied and understood with the same approach. We move systematically from pristine to highly oxidized and defective computational models, and we compare the simulation results with experimental data. Comparison with experiments is valuable also the other way around; this method allows us to verify that the simulated models are close to the real samples, which in turn makes simulated structures amenable to several computational experiments. Our results provide ab initio semiquantitative information and a new platform for extended insight into the structure and chemical composition of graphene-based materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Changing chemistry of particulate manganese in the near- and far-field hydrothermal plumes from 15°S East Pacific Rise and its influence on metal scavenging

Dissolved Mn(II) in the hydrothermal plume is known to be microbially oxidized to form Mn(III/IV) oxides, and the Mn oxides scavenge other trace elements in seawater. In the GEOTRACES GP16 cruise, dissolved Mn (dMn) and particulate Mn (pMn) were found to be transported over 4000 km westwards from the Southern Eastern Pacific Rise. Previous studies in this plume showed different removal rates of dMn and pMn as well as pMn size distribution between the near-field (<80 km from the ridge axis) and far-field (>80 km) plumes. In order to understand Mn cycling in these plumes, spatial distribution, oxidation states, and mineral structures of Mn in small size fraction (SSF; 0.8–51 μm) and large size fraction (LSF; >51 μm) particles from the near-field and far-field plumes were examined using micro X-ray fluorescence spectrometry (μ-XRF), X-ray absorption near-edge structure spectroscopy (XANES), chemical species mapping, and extended X-ray absorption fine-structure spectroscopy (EXAFS). In the near-field plume, pMn in the SSF is dominated by oxidized Mn with Mn(III) fractions of ~30%. They are a mixture of δ-MnO 2 and triclinic birnessites that is known to be formed as a result of autocatalytic Mn(II) oxidation at the surface of freshly-formed δ-MnO2, suggesting that both microbial and autocatalytic Mn oxidation occur in the near-field plume. The LSF pMn in the near-field plume is also oxidized and often found in large aggregates several hundreds of μm in size. These aggregates settle out in the near-field and during transport, and are not found in the far-field plume. In the far-field plume where Mn oxides are not newly formed, pMn in the SSF is oxidized, but their Mn(III) fractions are smaller than in the near-field pMn. Unlike the SSF, the far-field plume LSF pMn is dominated by reduced Mn, implying very slow aggregation of pMn in the far-field plume. The different characteristics of pMn between the near-field and far-field plumes affect its scavenging of other trace elements. In the near-field plume, Co, Mo, 231 Pa are associated with pMn, but not in the far-field plume. 231 Pa is adsorbed to pFe rather than pMn in the far-field plume, and Pb is adsorbed to pFe in the entire plume. The result shows that freshly-formed Mn oxides in the near-field plume have higher scavenging capacity than the far-field plume pMn. Our findings suggest that the mineralogical age of Mn oxides may be an important parameter that controls the scavenging of many other trace elements and isotopes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

In situ x-ray absorption investigations of a heterogenized molecular catalyst and its interaction with a carbon nanotube support

A highly active heterogenized molecular CO 2 reduction catalyst on a conductive carbon support is investigated to identify if its improved catalytic activity can be attributed to strong electronic interactions between catalyst and support. The molecular structure and electronic character of a [Re +1 (tBu-bpy)(CO) 3 Cl] (tBu-bpy = 4,4'-tert-butyl-2,2'-bipyridine) catalyst deposited on multiwalled carbon nanotubes are characterized using Re L 3 -edge x-ray absorption spectroscopy under electrochemical conditions and compared to the homogeneous catalyst. The Re oxidation state is characterized from the near-edge absorption region, while structural changes of the catalyst are assessed from the extended x-ray absorption fine structure under reducing conditions. Chloride ligand dissociation and a Re-centered reduction are both observed under applied reducing potential. The results confirm weak coupling of [Re(tBu-bpy)(CO) 3 Cl] with the support, since the supported catalyst exhibits the same oxidation changes as the homogeneous case. However, these results do not preclude strong interactions between a reduced catalyst intermediate and the support, preliminarily investigated here using quantum mechanical calculations. Thus, our results suggest that complicated linkage schemes and strong electronic interactions with the initial catalyst species are not required to improve the activity of heterogenized molecular catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Carbon nanotube coated metal mesh: Bridging nanoscale and macroscale

A novel hybrid structure has been developed by growing carbon nanotubes (CNTs) on a metal mesh that functions as a literally unlimitedly extendable backbone. This hybrid material structure provides a new approach of extending CNTs’ advantageous properties such as ultrahigh thermal and electrical conductivities, high sensitivity to gases, and distinctive wettability for different liquids with chemical inertness to macroscale—otherwise available only in nano- and microscales. In this feasibility work, CNTs were grown on a Type 316 stainless steel (SS) mesh by self-catalytical chemical vapor deposition (CVD) without the need of an externally added catalyst or catalyst support. For the radially aligned and entangled CNT forest on the SS mesh, the average CNT diameter is around 50 nm, while the length varies from 20 to 25 µm. High-resolution transmission electron microscopy analysis revealed the multiwall structure of the CNTs with >30 rolled-up graphitic sheets. Raman spectra of the CNTs showed a dominant G band, indicating a well-ordered graphitic nanostructure. Being highly hydrophobic with a water contact angle of ∼145° and oleophilic, the CNT-coated SS mesh could be used in fluid separation and organic contaminant removal from water. Moreover, CNTs are recognized for their exceptional thermal conductivity and the CNT-coated mesh offers a supportive structure with directly connected CNTs for efficient heat transfer. Proof of concept has been achieved for the CNT-coated mesh’s potentials as a liquid filter and an thermal interface material (TIM). Specifically, the CNT-coated mesh demonstrated the capability of capturing water from a water-organic mixture with a 100 % efficiency while allowing organic liquids to pass through the filter. Furthermore, when used as a TIM, the CNT-coated mesh reduced the interfacial thermal impedance by >30 %.

Carbon nanotubes (CNTS)↗

Active learning of ternary alloy structures and energies

Abstract Machine learning models with uncertainty quantification have recently emerged as attractive tools to accelerate the navigation of catalyst design spaces in a data-efficient manner. Here, we combine active learning with a dropout graph convolutional network (dGCN) as a surrogate model to explore the complex materials space of high-entropy alloys (HEAs). We train the dGCN on the formation energies of disordered binary alloy structures in the Pd-Pt-Sn ternary alloy system and improve predictions on ternary structures by performing reduced optimization of the formation free energy, the target property that determines HEA stability, over ensembles of ternary structures constructed based on two coordinate systems: (a) a physics-informed ternary composition space, and (b) data-driven coordinates discovered by the Diffusion Maps manifold learning scheme. Both reduced optimization techniques improve predictions of the formation free energy in the ternary alloy space with a significantly reduced number of DFT calculations compared to a high-fidelity model. The physics-based scheme converges to the target property in a manner akin to a depth-first strategy, whereas the data-driven scheme appears more akin to a breadth-first approach. Both sampling schemes, coupled with our acquisition function, successfully exploit a database of DFT-calculated binary alloy structures and energies, augmented with a relatively small number of ternary alloy calculations, to identify stable ternary HEA compositions and structures. This generalized framework can be extended to incorporate more complex bulk and surface structural motifs, and the results demonstrate that significant dimensionality reduction is possible in thermodynamic sampling problems when suitable active learning schemes are employed.

Chemistry↗

3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties

Abstract Motivation BISCAP is a state-of-the-art tool for automatically characterizing biofilm images obtained from Optical Coherence Tomography. Limited availability of other software tools is reported in the field. BISCAP’s first version processes 2D images only. Processing 3D images is a problem of greater scientific relevance since it deals with the entire structure of biofilms instead of their 2D slices. Results Building on the image-processing principles and algorithms proposed earlier for 2D images, these were adapted to the 3D case, and a more general implementation of BISCAP was developed. The primary goal concerns the extension of the initial methodology to incorporate the depth axis in 3D images; multiple improvements were also made to boost computational performance. The calculation of structural properties and visual outputs was extended to offer new insights into the 3D structure of biofilms. BISCAP was tested using 3D images of biofilms with different morphologies, consistently delivering accurate characterizations of 3D structures in a few minutes using standard laptop machines. Low user dependency is required for image analysis. Availability and implementation BISCAP is available from https://github.com/diogonarciso/BISCAP. All images used in the tutorials and the validation examples are available from https://web.fe.up.pt/∼fgm/biscap3d.

Narciso, Diogo A. C. (ORCID:0000000227767477)↗